Despite the Ends’ attack on Verlina being successfully repelled, the war has not yet ended. With the monster armies regrouping, the Black King tightens his grasp on the already conquered territory. New conflicts erupt all across Orte, as its remaining forces struggle to retain control over long-oppressed demi-human races. While Ends grow more potent each day, Toyohisa Shimazu remains unconscious after heavy injuries suffered during the Battle of Verlina. Facing enemies on every side, humanity’s fate is still on a knife's edge.

The entire countryside comes to a halt midday to witness a rare solar eclipse that is rumored to allow the average person to see Mushi. Unable to avert their gaze, the air is full of awe and wonder—but those who know the Mushi are preparing for the eclipse's aftermath. Based on a prediction from Tanyuu Karibusa, the cursed recorder, Mushishi Ginko finds himself in a very unlucky farming village. Immediately following the solar eclipse, a strange black cloud begins to gather in the sky and blocks the sun once more. Suspecting it to be the work of a Mushi known as Hihami, Ginko seeks to liberate the village from perpetual darkness. However, it seems that not all of the villagers are eager to return to the light.

After the fierce battle on Rakuyou, the untold past and true goal of the immortal Naraku leader, Utsuro, are finally revealed. By corrupting the Altana reserves of several planets, Utsuro has successfully triggered the intervention of the Tendoshuu’s greatest enemy: the Altana Liberation Army. With Earth as the main battleground in this interplanetary war, Utsuro's master plan to destroy the planet—and himself—is nearly complete. An attack on the O-Edo Central Terminal marks the beginning of the final battle to take back the land of the samurai. With the Yorozuya nowhere in sight, the bakufu all but collapsed, and the Shogun missing, the people are left completely helpless as the Liberation Army begins pillaging Edo in the name of freeing them from the Tendoshuu's rule. Caught in the crossfire between two equally imposing forces, can Gintoki, Kagura, Shinpachi, and the former students of Shouyou Yoshida put aside their differences and unite their allies to protect what they hold dear?

Human beings can be divided into two kinds: ordinary people who work for the living, and the undead who work for the dead. For the undead, their lives are dedicated to fulfilling the final wishes of ghosts who died with regrets. As for Baili Dengfeng, he has one and only one destiny in this world: to find his long-missing wife Ruyan. During his quest, Dengfeng makes acquaintance with Jia Xuan, whose family was murdered and is yet to be avenged, Liang You who is cute, naughty and adores him very much, and Liang Yuan, who simply doubts everything neurotically. After a series of events, he also learns of the existence of Spirit Masters and Spirit Slaves, and gets in touch with a mystical organization named "Spirits Expelling Order". With more and more mysteries being unveiled, the truth is drawing closer and closer to Dengfeng, who perhaps would rather not face the whole of it.